Expression of the beta3 tubulin gene (beta Tub60D) in the visceral mesoderm of Drosophila is dependent on a complex enhancer that binds Tinman and UBX

The effects of cadmium on the development of Drosophila and its transgenerational inheritance effects

A new focus in toxicology research is the impact of parental exposure to environmental toxic substances on the characteristics of offspring. In the present study, newly produced eggs of Drosophila melanogaster were treated with different concentrations of cadmium (0, 1, 2, 4, 8 mg/kg) to study the effects of development. The results showed that cadmium changed the larval body length and weight, prolonged the pupation and eclosion time, and changed the relative expression levels of development-related genes (baz, β-Tub60D, tj). Furthermore, the parental Drosophila (F₀) were treated with cadmium (4.5 mg/kg) from egg stage, and when grows to adults, they mated in standard medium to produce the de-stressed offspring (F₁-F₄) to assess the transgenerational effects of developmental delay. The results showed that the delayed effects of the pupation and eclosion time could be maintained for two generations, and the inhibiting effects of juvenile hormone (JH) and ecdysone (20-hydroxyecdysone, 20E) could be maintained for two or three generations. More importantly, cadmium increased the expression of DNA methylation-related genes (dDnmt2, dMBD2/3) in the ovaries (F₀-F₂) and testicles (F₀ and F₁). In addition, cadmium accumulated in parental Drosophila (F₀) was not transmitted to offspring through reproductive pathway. These results demonstrate that the developmental toxicity caused by cadmium could be transmitted to the de-stressed offspring, and the observed transgenerational inheritance effects may be associated with epigenetic regulation, underscoring the need to consider fitness of future generations in evaluating the toxicity and environmental risks of cadmium.

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila

During development cells become restricted in their differentiation potential by repressing alternative cell fates, and the Polycomb complex plays a crucial role in this process. However, how alternative fate genes are lineage-specifically silenced is unclear. We studied Ultrabithorax (Ubx), a multi-lineage transcription factor of the Hox class, in two tissue lineages using sorted nuclei and interfered with Ubx in mesodermal cells. We find that depletion of Ubx leads to the de-repression of genes normally expressed in other lineages. Ubx silences expression of alternative fate genes by retaining the Polycomb Group protein Pleiohomeotic at Ubx targeted genomic regions, thereby stabilizing repressive chromatin marks in a lineage-dependent manner. Our study demonstrates that Ubx stabilizes lineage choice by suppressing the multipotency encoded in the genome via its interaction with Pho. This mechanism may explain why the Hox code is maintained throughout the lifecycle, since it could set a block to transdifferentiation in adult cells.

Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures

The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP) from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ∼50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

The Drosophila homeodomain protein Tinman was the first transcription factor found to control the development and differentiation of the heart in any species. In spite of that, our knowledge of the number, identities, and mode of regulation of the downstream target genes of Tinman that are necessary to exert its cardiogenic functions is still very incomplete. To address these issues, we have performed a genome-wide analysis of DNA regions associated with Tinman-binding in embryos and the genes linked to them. The combined data from our in-depth in vivo assays of sequence elements with high Tinman occupancy allow the following general conclusions: (1) The majority of such sequences are active as regulatory elements (called enhancers) in mesodermal tissues that include Tinman-expressing cells. (2) The enhancers active in the heart progenitor cells and the heart generally are dependent on tinman gene activity, whereas those active in non-cardiac mesoderm are often bound neutrally by Tinman. (3) Tinman binding motifs in most cases are essential for cardiac enhancer activity, but in some cases they can be functionally-redundant with those of other cardiogenic factors. (4) Tinman-occupied cardiac enhancers are enriched for a newly discovered binding motif for an unknown factor that is functional in vivo.

Drosophila models of cardiac disease

The fruit fly Drosophila melanogaster has emerged as a useful model for cardiac diseases, both developmental abnormalities and adult functional impairment. Using the tools of both classical and molecular genetics, the study of the developing fly heart has been instrumental in identifying the major signaling events of cardiac field formation, cardiomyocyte specification, and the formation of the functioning heart tube. The larval stage of fly cardiac development has become an important model system for testing isolated preparations of living hearts for the effects of biological and pharmacological compounds on cardiac activity. Meanwhile, the recent development of effective techniques to study adult cardiac performance in the fly has opened new uses for the Drosophila model system. The fly system is now being used to study long-term alterations in adult performance caused by factors such as diet, exercise, and normal aging. The fly is a unique and valuable system for the study of such complex, long-term interactions, as it is the only invertebrate genetic model system with a working heart developmentally homologous to the vertebrate heart. Thus, the fly model combines the advantages of invertebrate genetics (such as large populations, facile molecular genetic techniques, and short lifespan) with physiological measurement techniques that allow meaningful comparisons with data from vertebrate model systems. As such, the fly model is well situated to make important contributions to the understanding of complicated interactions between environmental factors and genetics in the long-term regulation of cardiac performance.

Hox specificity unique roles for cofactors and collaborators

Hox proteins are well known for executing highly specific functions in vivo, but our understanding of the molecular mechanisms underlying gene regulation by these fascinating proteins has lagged behind. The premise of this review is that an understanding of gene regulation-by any transcription factor-requires the dissection of the cis-regulatory elements that they act upon. With this goal in mind, we review the concepts and ideas regarding gene regulation by Hox proteins and apply them to a curated list of directly regulated Hox cis-regulatory elements that have been validated in the literature. Our analysis of the Hox-binding sites within these elements suggests several emerging generalizations. We distinguish between Hox cofactors, proteins that bind DNA cooperatively with Hox proteins and thereby help with DNA-binding site selection, and Hox collaborators, proteins that bind in parallel to Hox-targeted cis-regulatory elements and dictate the sign and strength of gene regulation. Finally, we summarize insights that come from examining five X-ray crystal structures of Hox-cofactor-DNA complexes. Together, these analyses reveal an enormous amount of flexibility into how Hox proteins function to regulate gene expression, perhaps providing an explanation for why these factors have been central players in the evolution of morphological diversity in the animal kingdom.

Shaping segments: Hox gene function in the genomic age

Despite decades of research, morphogenesis along the various body axes remains one of the major mysteries in developmental biology. A milestone in the field was the realisation that a set of closely related regulators, called Hox genes, specifies the identity of body segments along the anterior-posterior (AP) axis in most animals. Hox genes have been highly conserved throughout metazoan evolution and code for homeodomain-containing transcription factors. Thus, they exert their function mainly through activation or repression of downstream genes. However, while much is known about Hox gene structure and molecular function, only a few target genes have been identified and studied in detail. Our knowledge of Hox downstream genes is therefore far from complete and consequently Hox-controlled morphogenesis is still poorly understood. Genome-wide approaches have facilitated the identification of large numbers of Hox downstream genes both in Drosophila and vertebrates, and represent a crucial step towards a comprehensive understanding of how Hox proteins drive morphological diversification. In this review, we focus on the role of Hox genes in shaping segmental morphologies along the AP axis in Drosophila, discuss some of the conclusions drawn from analyses of large target gene sets and highlight methods that could be used to gain a more thorough understanding of Hox molecular function. In addition, the mechanisms of Hox target gene regulation are considered with special emphasis on recent findings and their implications for Hox protein specificity in the context of the whole organism.

Transcriptional activation by extradenticle in the Drosophila visceral mesoderm

decapentaplegic (dpp) is a direct target of Ultrabithorax (Ubx) in parasegment 7 (PS7) of the embryonic visceral mesoderm. We demonstrate that extradenticle (exd) and homothorax (hth) are also required for dpp expression in this location, as well as in PS3, at the site of the developing gastric caecae. A 420 bp element from dpp contains EXD binding sites necessary for expressing a reporter gene in both these locations. Using a specificity swap, we demonstrate that EXD directly activates this element in vivo. Activation does not require Ubx, demonstrating that EXD can activate transcription independently of homeotic proteins. Restoration is restricted to the domains of endogenous dpp expression, despite ubiquitous expression of altered specificity EXD. We demonstrate that nuclear EXD is more extensively phosphorylated than the cytoplasmic form, suggesting that EXD is a target of signal transduction by protein kinases.

Identification of genetic loci that interact with cut during Drosophila wing-margin development

The Drosophila selector gene cut is a hierarchal regulator of external sensory organ identity and is required to pattern the sensory and nonsensory cells of the wing margin. Cut performs the latter function, in part, by maintaining expression of the secreted morphogen encoded by wingless (wg). We find that Cut is required for wing-margin sensory organ specification in addition to and independently of Wg maintenance. In addition, we performed a genetic modifier screen to identify other genes that interact with cut in the regulation of wing-margin patterning. In total, 45 genetic loci (35 gain-of-function and 10 loss-of-function loci) were identified by virtue of their ability to suppress the wing-margin defects resulting from gypsy retrotransposon-mediated insulation of the cut wing-margin enhancer. Further genetic characterization identified several subgroups of candidate cut interacting loci. One group consists of putative regulators of gypsy insulator activity. A second group is potentially required for the regulation of Cut expression and/or activity and includes longitudinals lacking, a gene that encodes a family of BTB-domain zinc-finger transcription factors. A third group, which includes a component of the Brahma chromatin remodeling complex encoded by moira, affects the level of Cut expression in two opposing ways by suppressing the gypsy-mediated ct(K) phenotype and enhancing the non-gypsy ct(53d) phenotype. This suggests that the Brahma complex modulates both enhancer-controlled transcription and gypsy-mediated gene insulation of the cut locus.

Transcription of Drosophila troponin I gene is regulated by two conserved, functionally identical, synergistic elements

The Drosophila wings-up A gene encodes Troponin I. Two regions, located upstream of the transcription initiation site (upstream regulatory element) and in the first intron (intron regulatory element), regulate gene expression in specific developmental and muscle type domains. Based on LacZ reporter expression in transgenic lines, upstream regulatory element and intron regulatory element yield identical expression patterns. Both elements are required for full expression levels in vivo as indicated by quantitative reverse transcription-polymerase chain reaction assays. Three myocyte enhancer factor-2 binding sites have been functionally characterized in each regulatory element. Using exon specific probes, we show that transvection is based on transcriptional changes in the homologous chromosome and that Zeste and Suppressor of Zeste 3 gene products act as repressors for wings-up A. Critical regions for transvection and for Zeste effects are defined near the transcription initiation site. After in silico analysis in insects (Anopheles and Drosophila pseudoobscura) and vertebrates (Ratus and Coturnix), the regulatory organization of Drosophila seems to be conserved. Troponin I (TnI) is expressed before muscle progenitors begin to fuse, and sarcomere morphogenesis is affected by TnI depletion as Z discs fail to form, revealing a novel developmental role for the protein or its transcripts. Also, abnormal stoichiometry among TnI isoforms, rather than their absolute levels, seems to cause the functional muscle defects.

Posterior migration of the salivary gland requires an intact visceral mesoderm and integrin function

The final overall shape of an organ and its position within the developing embryo arise as a consequence of both its intrinsic properties and its interactions with surrounding tissues. Here, we focus on the role of directed cell migration in shaping and positioning the Drosophila salivary gland. We demonstrate that the salivary gland turns and migrates along the visceral mesoderm to become properly oriented with respect to the overall embryo. We show that salivary gland posterior migration requires the activities of genes that position the visceral mesoderm precursors, such as heartless, thickveins, and tinman, but does not require a differentiated visceral mesoderm. We also demonstrate a role for integrin function in salivary gland migration. Although the mutations affecting salivary gland motility and directional migration cause defects in the final positioning of the salivary gland, most do not affect the length or diameter of the salivary gland tube. These findings suggest that salivary tube dimensions may be an intrinsic property of salivary gland cells.

Transcription factors in cardiogenesis: the combinations that unlock the mysteries of the heart

Heart formation is one of the first signs of organogenesis within the developing embryo and this process is conserved from flies to man. Completing the genetic roadmap of the molecular mechanisms that control the cell specification and differentiation of cells that form the developing heart has been an exciting and fast-moving area of research in the fields of molecular and developmental biology. At the core of these studies is an interest in the transcription factors that are responsible for initiation of a pluripotent cell to become programmed to the cardiac lineage and the subsequent transcription factors that implement the instructions set up by the cells commitment decision. To gain a better understanding of these pathways, cardiac-expressed transcription factors have been identified, cloned, overexpressed, and mutated to try to determine function. Although results vary depending on the gene in question, it is clear that there is a striking evolutionary conservation of the cardiogenic program among species. As we move up the evolutionary ladder toward man, we encounter cases of functional redundancy and combinatorial interactions that reflect the complex networks of gene expression that orchestrate heart development. This review focuses on what is known about the transcription factors implicated in heart formation and the role they play in this intricate genetic program.

Increased levels of tyrosinated alpha-, beta(III)-, and beta(IV)-tubulin isotypes in paclitaxel-resistant MCF-7 breast cancer cells

Paclitaxel (PTX), the diterpene alkaloid, is a potent anti-cancer drug and is routinely used for the treatment of breast and ovarian cancers. The cellular targets of PTX are microtubules, which are composed of alpha- and beta-tubulin. Development of PTX resistance in patients has been a major problem associated with cancer chemotherapy. In an effort to get insight into this phenomenon of drug resistance, a PTX-resistant cell line from MCF-7 breast cancer cells has been generated. Western analysis of the cell extracts revealed that the resistant cells contain 2-fold higher amount of tyrosinated alpha-tubulin than those of the wild-type MCF-7 cells. Similar analyses of beta-tubulin with the isotype-specific monoclonal antibodies demonstrated that the PTX-resistant cells contain 2.5-fold higher amounts of beta(III) and 1.5-fold higher amount of beta(IV)-tubulin, while no difference was observed in the level of beta(I) isotype. These results demonstrate for the first time that PTX resistance is associated with an increase in the level of tyrosinated alpha-tubulin.

Tinman regulates the transcription of the beta3 tubulin gene (betaTub60D) in the dorsal vessel of Drosophila

During Drosophila embryogenesis, the beta3 tubulin gene is expressed in the visceral and somatic mesoderm as well as in the dorsal vessel. Transcription of the gene is limited to four pairs of cardioblasts per segment. Here we show that its expression in the dorsal vessel (dv) is mediated by a 333-bp enhancer located upstream of the gene. The homeodomain protein Tinman is also expressed in these cardioblasts, implying that Tinman might be a key regulator of the beta3 tubulin gene. Gel retardation and footprint assays indeed revealed two Tinman binding sites within the dv-specific enhancer. We analyzed the relevance of the Tinman binding sites in a transgenic fly assay and observed distinct functions for both sites. The BS(Tin-1460) site is absolutely required for expression in cardioblasts, while BS(Tin-1425) is needed for high-level expression. Thus, these two Tinman binding sites act in concert to drive beta3 tubulin gene expression during heart development. Tinman initially functions in the specification of visceral mesoderm and heart progenitors, but remains expressed in cardioblasts until dorsal closure. Overall, our data demonstrate a late function for Tinman in the regulation of beta3 tubulin gene expression in the forming heart of Drosophila.